Cream cheese is difficult to manufacture. Normally, protein molecules in milk have a negative surface charge, which keeps milk in a liquid state; the molecules act as surfactants, forming micelles around the particles of fat and keeping it in emulsion. Lactic acid bacteria are added to pasteurized and homogenized milk. During the fermentation at around 23 °C, the pH levelof the milk decreases. Amino acids at the surface of the proteins beginlosing charge and become neutral, turning the fat micelles from hydrophilic to hydrophobic state and causing the liquid to coagulate.If the bacteria are left in the milk too long, the pH lowers further,the micelles attain a positive charge and the mixture returns to liquidform. The key then is to kill the bacteria by heating the mixture to52-63 °C at the moment the cheese is in an isoelectric point,meaning the state at which half the ionizable surface amino acids ofthe proteins are positively charged and half are negative. Inaccuratetiming of heating leads to an inferior or unusable product.

However, subtle changes in the timing of the process can result invariations in flavor and texture. Furthermore, because cream cheese hasa higher fat content than other cheeses and fat repels water, which tends to separate from the cheese, stabilizers such as guar and carob gums must be added to prolong its shelf life.

Improper heat treatment of milk may lead to formation of hardparticles of amorphous compacted protein, causing unpleasant grittiness.